Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pooled CRISPR/Cas9 screen for genes that contribute to ribosome biogenesis and turnover

ABSTRACT: While features of ribosome assembly are shared between species, our understanding of the diversity, complexity, dynamics, and regulation of ribosome production in multicellular organisms remains incomplete. To gain insights into ribosome biogenesis in human cells, we performed a genome wide loss of function screen combined with differential labeling of pre-existing and newly assembled ribosomes. These efforts identified two functionally uncharacterized genes, C1ORF09 and SPATA5. We provide evidence that these factors, together with CINP and SPATA5L1, control a late step of human pre-60S maturation in the cytoplasm. Loss of either C1ORF109 or SPATA5 impairs global protein synthesis. These results link ribosome assembly with neurodevelopmental disorders associated with recessive SPATA5 mutations. Based on these findings, we propose the expanded repertoire of ribosome biogenesis factors likely enables multicellular organisms to coordinate multiple steps of ribosome production in response to different developmental and environmental stimuli.

ORGANISM(S): Homo sapiens

PROVIDER: GSE197277 | GEO | 2022/02/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The RNA helicases Has1, Mak5 and Spb4 mediate diverse functions at distinct regions of pre-ribosomal complexes

Project description:Assembly of eukaryotic ribosomal subunits is a highly dynamic and energy-consuming process involving numerous structural and compositional changes. Here, we identify the pre-ribosomal binding sites of three ATP-dependent RNA helicases Has1, Mak5 and Spb4 and by elucidating the precise targets of these enzymes, we uncover direct roles of Has1 in mediating release of the U14 snoRNA and dissociation of a cluster of early pre-60S biogenesis factors. We further discover pre-rRNA remodelling by Mak5 enables recruitment of the ribosomal protein Rpl10 in the cytoplasm and show that binding of Spb4 to a molecular hinge at the base of ES27 facilitates binding of the export adaptor Arx1 to pre-60S complexes. Our data highlight RNA helicases as key regulators of critical events during ribosome biogenesis and provide novel insights into the structural remodelling events that take place during assembly of the ribosomal subunits.

2018-12-19 | GSE109216 | GEO

The Ribosome Assembly Factor Reh1 is Released from the Polypeptide Exit Tunnel in the Pioneer Round of Translation

Project description:In S. cerevisiae, the ribosome assembly factor Reh1 binds to pre-60S subunits at a late stage during their cytoplasmic maturation. Unlike canonical assembly factors, which associate exclusively with pre-60S subunits, we observed that Reh1 sediments with polysomes in addition to free 60S subunits. We therefore investigated the intriguing possibility that Reh1 remains associated with 60S subunits after the release of the anti-association factor Tif6 and after subunit joining. Here, we show that Reh1-bound nascent 60S subunits associate with 40S subunits to form actively translating ribosomes.

2024-01-24 | GSE246163 | GEO

The RNA helicase Dbp10 coordinates assembly factor association with PTC formation during ribosome biogenesis

Project description:During ribosome biogenesis a plethora of assembly factors and essential enzymes drive the unidirectional maturation of nascent pre-ribosomal subunits. The DEAD-box RNA helicase Dbp10 is suggested to restructure pre-ribosomal rRNA of the evolving peptidyl-transferase center (PTC) on nucleolar ribosomal 60S assembly intermediates. Here, we show that point mutations within conserved catalytic helicase-core motifs of Dbp10 yield a dominant-lethal growth phenotype. Such dbp10 mutants, which stably associate with pre-60S intermediates, impair pre-60S biogenesis at a nucleolar stage prior to the release of assembly factor Rrp14 and stable integration of late nucleolar factors such as Noc3. Furthermore, the binding of the GTPase Nug1 to particles isolated directly via mutant Dbp10 bait proteins is specifically inhibited. The N-terminal domain of Nug1 interacts with Dbp10 and the methyltransferase Spb1, whose pre-60S incorporation is also reduced in absence of functional Dbp10. Our data suggest that Dbp10’s helicase activity generates a crucial framework for assembly factor docking thereby permitting the progression of pre-60S maturation

2024-05-22 | PXD046068 | Pride

The E3 SUMO ligase Mms21 controls ribosome biogenesis

Project description:The budding yeast E3 SUMO ligase Mms21, a component of the Smc5-6 complex, regulates sister chromatid cohesion, DNA replication, and DNA repair. We identify a role for Mms21 in ribosome biogenesis. The mms21RINGD mutant exhibits reduced rRNA production, nuclear accumulation of 60S and 40S ribosomal proteins, and elevated Gcn4 translation. Genes involved in ribosome biogenesis and translation are down-regulated in the mms21RINGD mutant. Examining gene expression profile of mms21RINGD mutant compared to wild-type by RNA Seq using Ilumina sequencing

2015-06-13 | E-GEOD-69826 | biostudies-arrayexpress

Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans.

Project description:Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their role in human health and disease remains obscure. Here, we show that circular antisense non-coding RNA in the INK4 locus (circANRIL), which is transcribed at a locus of atherosclerotic cardiovascular disease on chromosome 9p21, confers athero-protection by controlling ribosomal RNA (rRNA) maturation and modulating pathways of atherogenesis. At the molecular level, circANRIL competes with precursor rRNA (pre-rRNA) for binding to pescadillo homolog 1 (PES1), an essential 60S-preribosomal assembly factor, thereby impairing exonuclease-mediated pre-rRNA processing and ribosome biogenesis. As a consequence, circANRIL induces nucleolar stress and p53 activation, resulting in the induction of apoptosis and inhibition of proliferation, which are key athero-protective cell functions within the arterial wall. Collectively, these findings identify circANRIL as a prototype of a circRNA regulating ribosome biogenesis and conferring athero-protection, thereby unveiling a therapeutic potential of certain circRNAs in human disease. Analysis of transcriptome-wide expression level in HEK293 cells with stable overexpression of circular ANRIL (n=3) compared to a vector control (n=3).

2016-08-22 | E-GEOD-65392 | biostudies-arrayexpress

The translation release factor methyltransferase Mtq2-Trm112 is required for ribosome biogenesis

Project description:The Mtq2-Trm112 methyltransferase is known to modify the translational eukaryotic release factor eRF1 on the glutamine side chain of a universally conserved GGQ motif, which is essential to translation termination. The exact role of eRF1 methylation remains unknown. As the deletion of MTQ2 leads to severe growth impairment in S. cerevisiae, we have investigated its role further. Here we report an unexpected function of Mtq2 in ribosome biogenesis. We reveal that Mtq2 is part of nuclear precursor ribosomes to 60S subunits, and we demonstrate that its catalytic activity is required for the stable production of mature 5.8S and 25S rRNAs and for pre-60S export. Consistently, in the absence of Mtq2 function pre-60S subunits enriched in the export factors Nmd3 and Arx1 accumulate in the nucleus. We conclude that, in addition to its role as a translation terminator modification enzyme, Mtq2 is a ribosome assembly factor which is important for late-stage large ribosomal subunit formation.

2020-10-12 | PXD018733 | Pride

A comprehensive landscape of 60S ribosome biogenesis factors

Project description:We used quantitative proteomics and crosslinking mass spectrometry (XL-MS) to analyse a comprehensive set of purified pre-60S ribosomal particles, obtaining a detailed timeline of RBF engagement during 60S ribosome biogenesis as well as particle-specific crosslink networks for all analysed particles. Our data provide an important resource for all future structural and biochemical studies of 60S ribosome biogenesis.

2021-12-07 | PXD021831 | Pride

The E3 SUMO ligase Mms21 controls ribosome biogenesis

2015-06-13 | GSE69826 | GEO

The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly

Project description:Early pre-60S ribosomal particles are poorly characterized, highly dynamic complexes that undergo extensive rRNA folding and compaction concomitant with assembly of ribosomal proteins and exchange of assembly factors. Pre-60S particles contain numerous RNA helicases, which are likely regulators of accurate and efficient formation of appropriate rRNA structures. Here we reveal binding of the RNA helicase Dbp7 to domain V/VI of early pre-60S particles in yeast and show that in the absence of this protein, dissociation of the Npa1 scaffolding complex, release of the snR190 folding chaperone, recruitment of the A3 cluster factors and binding of the ribosomal protein uL3 are impaired. uL3 is critical for formation of the peptidyltransferase center and is responsible for stabilizing interactions between the 5’ and 3’ ends of the 25S, an essential pre-requisite for subsequent pre-60S maturation events. Highlighting the importance of pre-ribosome remodeling by Dbp7, our data suggest that in the absence of Dbp7 or its catalytic activity, early pre-ribosomal particles are targeted for degradation.

2021-08-18 | GSE160734 | GEO

The RNA helicase Dbp7 promotes domain VI compaction and stabilization of inter-domain interactions during early 60S assembly

2021-08-16 | GSE161347 | GEO